Multiple sequence alignment - TraesCS4A01G208800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G208800 chr4A 100.000 4201 0 0 2234 6434 501968494 501972694 0.000000e+00 7758.0
1 TraesCS4A01G208800 chr4A 100.000 1842 0 0 1 1842 501966261 501968102 0.000000e+00 3402.0
2 TraesCS4A01G208800 chr4A 100.000 577 0 0 6552 7128 501972812 501973388 0.000000e+00 1066.0
3 TraesCS4A01G208800 chr4D 98.177 2908 40 7 3534 6434 89429574 89432475 0.000000e+00 5064.0
4 TraesCS4A01G208800 chr4D 93.757 1682 60 18 54 1725 89426725 89428371 0.000000e+00 2483.0
5 TraesCS4A01G208800 chr4D 98.007 1204 20 4 2274 3475 89428369 89429570 0.000000e+00 2087.0
6 TraesCS4A01G208800 chr4D 87.326 576 23 17 6577 7118 89432617 89433176 1.310000e-171 614.0
7 TraesCS4A01G208800 chr4D 84.043 94 14 1 6324 6416 486932222 486932129 9.850000e-14 89.8
8 TraesCS4A01G208800 chr4B 95.589 2947 105 15 3493 6422 126333490 126336428 0.000000e+00 4698.0
9 TraesCS4A01G208800 chr4B 93.725 1785 51 19 65 1834 126327348 126329086 0.000000e+00 2619.0
10 TraesCS4A01G208800 chr4B 96.745 1198 32 7 2277 3473 126330379 126331570 0.000000e+00 1989.0
11 TraesCS4A01G208800 chr4B 85.121 289 26 9 6832 7113 126505463 126505741 5.440000e-71 279.0
12 TraesCS4A01G208800 chr4B 83.799 179 9 13 6632 6791 126505284 126505461 1.240000e-32 152.0
13 TraesCS4A01G208800 chr4B 100.000 33 0 0 2252 2284 126329421 126329453 2.150000e-05 62.1
14 TraesCS4A01G208800 chr5B 75.000 1328 271 48 4253 5549 221903911 221905208 2.250000e-154 556.0
15 TraesCS4A01G208800 chr5B 81.746 252 44 2 240 490 222367015 222367265 7.250000e-50 209.0
16 TraesCS4A01G208800 chr5B 82.938 211 33 3 2601 2810 221902012 221902220 3.390000e-43 187.0
17 TraesCS4A01G208800 chr5B 100.000 64 0 0 1 64 9618113 9618176 1.260000e-22 119.0
18 TraesCS4A01G208800 chr5D 74.547 1324 281 46 4255 5549 208510803 208512099 1.760000e-145 527.0
19 TraesCS4A01G208800 chr5D 81.746 252 44 2 240 490 209309422 209309672 7.250000e-50 209.0
20 TraesCS4A01G208800 chr5D 84.000 200 30 2 2612 2810 208508991 208509189 2.620000e-44 191.0
21 TraesCS4A01G208800 chr5D 81.250 96 16 2 6324 6418 255076534 255076440 7.670000e-10 76.8
22 TraesCS4A01G208800 chr5A 81.349 252 45 2 240 490 270177402 270177652 3.370000e-48 204.0
23 TraesCS4A01G208800 chr5A 82.524 206 35 1 2605 2810 269276275 269276479 5.680000e-41 180.0
24 TraesCS4A01G208800 chr5A 84.536 97 13 2 6324 6418 667304886 667304790 2.120000e-15 95.3
25 TraesCS4A01G208800 chr5A 81.443 97 14 3 6324 6418 338287883 338287789 7.670000e-10 76.8
26 TraesCS4A01G208800 chr6D 100.000 66 0 0 1 66 284851800 284851865 9.710000e-24 122.0
27 TraesCS4A01G208800 chr7B 98.529 68 1 0 1 68 712631956 712631889 3.490000e-23 121.0
28 TraesCS4A01G208800 chr3B 100.000 64 0 0 1 64 378720208 378720271 1.260000e-22 119.0
29 TraesCS4A01G208800 chr3B 96.774 62 2 0 5 66 765775660 765775721 3.520000e-18 104.0
30 TraesCS4A01G208800 chr2B 100.000 64 0 0 1 64 400625511 400625574 1.260000e-22 119.0
31 TraesCS4A01G208800 chr7A 98.438 64 1 0 1 64 519850843 519850906 5.840000e-21 113.0
32 TraesCS4A01G208800 chr7A 87.692 65 8 0 2 66 669770578 669770642 7.670000e-10 76.8
33 TraesCS4A01G208800 chr1B 86.905 84 11 0 6324 6407 565664554 565664637 2.120000e-15 95.3
34 TraesCS4A01G208800 chr1D 84.158 101 11 5 6320 6415 317439610 317439510 7.610000e-15 93.5
35 TraesCS4A01G208800 chr1A 83.333 102 11 6 6320 6415 398461006 398460905 9.850000e-14 89.8
36 TraesCS4A01G208800 chr2A 90.476 63 6 0 2 64 13123981 13124043 4.580000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G208800 chr4A 501966261 501973388 7127 False 4075.333333 7758 100.00000 1 7128 3 chr4A.!!$F1 7127
1 TraesCS4A01G208800 chr4D 89426725 89433176 6451 False 2562.000000 5064 94.31675 54 7118 4 chr4D.!!$F1 7064
2 TraesCS4A01G208800 chr4B 126327348 126336428 9080 False 2342.025000 4698 96.51475 65 6422 4 chr4B.!!$F1 6357
3 TraesCS4A01G208800 chr5B 221902012 221905208 3196 False 371.500000 556 78.96900 2601 5549 2 chr5B.!!$F3 2948
4 TraesCS4A01G208800 chr5D 208508991 208512099 3108 False 359.000000 527 79.27350 2612 5549 2 chr5D.!!$F2 2937

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
623 637 0.177836 TACATGGCTGTGATCACCGG 59.822 55.000 22.85 15.92 36.79 5.28 F
1680 1714 0.322726 TGCATGATCCTGTGTGGGTG 60.323 55.000 0.00 0.00 36.20 4.61 F
1684 1718 0.400213 TGATCCTGTGTGGGTGGAAC 59.600 55.000 0.00 0.00 36.20 3.62 F
3487 4462 2.094803 ACCAAATGTGTGTGTGTGTGTG 60.095 45.455 0.00 0.00 0.00 3.82 F
4863 7863 1.065126 AGGAGATTCTTTTGCGGGGAG 60.065 52.381 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 3443 0.460722 ATTGCAGCACAACAAGCACA 59.539 45.000 0.00 0.00 42.27 4.57 R
2979 3954 3.126514 CGAGAGCATGCAAAACAAGATCT 59.873 43.478 21.98 10.29 44.81 2.75 R
4255 7244 8.415950 TTTAATTTATTTGTCCTGCAGGAGAA 57.584 30.769 34.90 34.90 46.49 2.87 R
5189 8189 0.465824 ATTCTCTGCAGCCTCCATGC 60.466 55.000 9.47 0.00 44.11 4.06 R
6981 10044 1.264020 GTGTGTGCGTGTGAATGATGT 59.736 47.619 0.00 0.00 0.00 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.939974 TGGCTAGATTGACATCGTGC 58.060 50.000 0.00 0.00 34.17 5.34
23 24 1.206849 TGGCTAGATTGACATCGTGCA 59.793 47.619 0.00 0.00 35.52 4.57
24 25 1.863454 GGCTAGATTGACATCGTGCAG 59.137 52.381 0.00 0.00 35.52 4.41
25 26 1.260033 GCTAGATTGACATCGTGCAGC 59.740 52.381 0.00 0.00 34.61 5.25
26 27 2.819115 CTAGATTGACATCGTGCAGCT 58.181 47.619 0.00 0.00 34.17 4.24
27 28 1.366679 AGATTGACATCGTGCAGCTG 58.633 50.000 10.11 10.11 34.17 4.24
28 29 1.081892 GATTGACATCGTGCAGCTGT 58.918 50.000 16.64 0.00 30.94 4.40
29 30 1.061711 GATTGACATCGTGCAGCTGTC 59.938 52.381 16.64 13.62 44.02 3.51
30 31 1.284297 TTGACATCGTGCAGCTGTCG 61.284 55.000 16.64 19.39 46.01 4.35
31 32 1.734477 GACATCGTGCAGCTGTCGT 60.734 57.895 24.17 14.00 36.44 4.34
32 33 1.949015 GACATCGTGCAGCTGTCGTG 61.949 60.000 24.17 22.26 36.44 4.35
33 34 3.114616 ATCGTGCAGCTGTCGTGC 61.115 61.111 24.17 10.01 41.59 5.34
37 38 2.281002 TGCAGCTGTCGTGCATGT 60.281 55.556 16.64 0.00 45.96 3.21
38 39 1.005156 TGCAGCTGTCGTGCATGTA 60.005 52.632 16.64 0.00 45.96 2.29
39 40 1.015607 TGCAGCTGTCGTGCATGTAG 61.016 55.000 16.64 7.15 45.96 2.74
40 41 1.016130 GCAGCTGTCGTGCATGTAGT 61.016 55.000 16.64 0.00 40.86 2.73
41 42 0.717784 CAGCTGTCGTGCATGTAGTG 59.282 55.000 5.25 4.17 34.99 2.74
96 97 1.167851 CCACTGTGCCCAACTACATG 58.832 55.000 1.29 0.00 0.00 3.21
126 131 2.979813 GCAACAGCATAAAAACAGACGG 59.020 45.455 0.00 0.00 0.00 4.79
489 503 2.698763 GCTTTCCTCCTGCTGCTGC 61.699 63.158 8.89 8.89 40.20 5.25
490 504 1.002379 CTTTCCTCCTGCTGCTGCT 60.002 57.895 17.00 0.00 40.48 4.24
491 505 1.303074 TTTCCTCCTGCTGCTGCTG 60.303 57.895 17.00 15.58 40.48 4.41
492 506 3.914579 TTCCTCCTGCTGCTGCTGC 62.915 63.158 22.51 22.51 40.48 5.25
493 507 4.411981 CCTCCTGCTGCTGCTGCT 62.412 66.667 27.67 0.00 40.48 4.24
494 508 3.128188 CTCCTGCTGCTGCTGCTG 61.128 66.667 27.67 25.97 40.48 4.41
620 634 3.003068 GCTTGATACATGGCTGTGATCAC 59.997 47.826 19.27 19.27 36.79 3.06
623 637 0.177836 TACATGGCTGTGATCACCGG 59.822 55.000 22.85 15.92 36.79 5.28
625 639 3.635191 TGGCTGTGATCACCGGCA 61.635 61.111 32.90 32.90 45.68 5.69
711 725 3.136641 TCTCCAGGGCTTAAGAAGGAT 57.863 47.619 6.67 0.00 0.00 3.24
723 737 1.673168 AGAAGGATGAAGCCGAATGC 58.327 50.000 0.00 0.00 41.71 3.56
744 763 2.285969 ATGGGCTGGGCTCTCTGT 60.286 61.111 0.00 0.00 0.00 3.41
751 770 1.612726 GCTGGGCTCTCTGTTGTTGAT 60.613 52.381 0.00 0.00 0.00 2.57
759 778 4.560128 CTCTCTGTTGTTGATCCGAAAGA 58.440 43.478 0.00 0.00 0.00 2.52
760 779 5.152623 TCTCTGTTGTTGATCCGAAAGAT 57.847 39.130 0.00 0.00 38.17 2.40
761 780 6.280855 TCTCTGTTGTTGATCCGAAAGATA 57.719 37.500 0.00 0.00 34.42 1.98
762 781 6.333416 TCTCTGTTGTTGATCCGAAAGATAG 58.667 40.000 0.00 0.00 34.42 2.08
763 782 6.152831 TCTCTGTTGTTGATCCGAAAGATAGA 59.847 38.462 0.00 0.00 34.42 1.98
764 783 6.100004 TCTGTTGTTGATCCGAAAGATAGAC 58.900 40.000 0.00 0.00 34.42 2.59
765 784 6.037786 TGTTGTTGATCCGAAAGATAGACT 57.962 37.500 0.00 0.00 34.42 3.24
766 785 5.869344 TGTTGTTGATCCGAAAGATAGACTG 59.131 40.000 0.00 0.00 34.42 3.51
767 786 5.914898 TGTTGATCCGAAAGATAGACTGA 57.085 39.130 0.00 0.00 34.42 3.41
768 787 6.471233 TGTTGATCCGAAAGATAGACTGAT 57.529 37.500 0.00 0.00 34.42 2.90
775 804 4.499183 CGAAAGATAGACTGATATGGGCC 58.501 47.826 0.00 0.00 0.00 5.80
805 834 2.893215 TCCTGAACGAGGAGGTAGAA 57.107 50.000 0.00 0.00 46.96 2.10
806 835 2.724454 TCCTGAACGAGGAGGTAGAAG 58.276 52.381 0.00 0.00 46.96 2.85
807 836 2.307980 TCCTGAACGAGGAGGTAGAAGA 59.692 50.000 0.00 0.00 46.96 2.87
834 864 4.711355 CCATTGGGATAAAAGCTCAGGAAA 59.289 41.667 0.00 0.00 35.59 3.13
850 880 1.136110 GGAAAGAAGGAGAGCCGAGAG 59.864 57.143 0.00 0.00 39.96 3.20
851 881 0.534873 AAAGAAGGAGAGCCGAGAGC 59.465 55.000 0.00 0.00 44.25 4.09
1054 1084 1.084370 CCGCTTCCACAATCTCGACC 61.084 60.000 0.00 0.00 0.00 4.79
1218 1248 6.467047 CGATTTTCCTTCAGATGAATGTTTCG 59.533 38.462 0.00 0.00 33.01 3.46
1242 1272 2.419990 CCTGTGACCATTTCTATGCGGA 60.420 50.000 0.00 0.00 0.00 5.54
1246 1276 4.335315 TGTGACCATTTCTATGCGGAATTC 59.665 41.667 0.00 0.00 0.00 2.17
1270 1300 8.589335 TCTTTTTCGAGAATACATATAGCACC 57.411 34.615 0.00 0.00 0.00 5.01
1271 1301 8.201464 TCTTTTTCGAGAATACATATAGCACCA 58.799 33.333 0.00 0.00 0.00 4.17
1272 1302 8.902540 TTTTTCGAGAATACATATAGCACCAT 57.097 30.769 0.00 0.00 0.00 3.55
1274 1304 7.468141 TTCGAGAATACATATAGCACCATCT 57.532 36.000 0.00 0.00 0.00 2.90
1275 1305 8.575649 TTCGAGAATACATATAGCACCATCTA 57.424 34.615 0.00 0.00 0.00 1.98
1306 1340 9.498039 AAAGAAGATTTCTATGGGGAATTTCAT 57.502 29.630 0.00 0.00 39.61 2.57
1308 1342 9.140874 AGAAGATTTCTATGGGGAATTTCATTC 57.859 33.333 0.00 0.00 38.49 2.67
1425 1459 1.103803 TCCATTCCTCTCGGAGAACG 58.896 55.000 9.32 2.49 41.25 3.95
1453 1487 1.804151 GCAAATTTCCGCCCCTTTTTC 59.196 47.619 0.00 0.00 0.00 2.29
1471 1505 2.125310 CCCAACATGCGGACGCTA 60.125 61.111 18.04 4.87 42.51 4.26
1680 1714 0.322726 TGCATGATCCTGTGTGGGTG 60.323 55.000 0.00 0.00 36.20 4.61
1681 1715 1.033746 GCATGATCCTGTGTGGGTGG 61.034 60.000 0.00 0.00 36.20 4.61
1682 1716 0.620030 CATGATCCTGTGTGGGTGGA 59.380 55.000 0.00 0.00 36.20 4.02
1683 1717 1.004628 CATGATCCTGTGTGGGTGGAA 59.995 52.381 0.00 0.00 36.20 3.53
1684 1718 0.400213 TGATCCTGTGTGGGTGGAAC 59.600 55.000 0.00 0.00 36.20 3.62
1741 1775 7.402054 TGATTTATCTGCCAAGAACTAAAGGA 58.598 34.615 0.00 0.00 35.59 3.36
1742 1776 7.336931 TGATTTATCTGCCAAGAACTAAAGGAC 59.663 37.037 0.00 0.00 35.59 3.85
1743 1777 4.917906 ATCTGCCAAGAACTAAAGGACT 57.082 40.909 0.00 0.00 35.59 3.85
1744 1778 4.706842 TCTGCCAAGAACTAAAGGACTT 57.293 40.909 0.00 0.00 0.00 3.01
2287 3254 9.754382 TTGGTAACCGTAATCAGATTATTCTAC 57.246 33.333 6.14 6.25 0.00 2.59
2358 3325 4.060205 GTTTGCCATCTTGCATTGACTTT 58.940 39.130 0.00 0.00 41.70 2.66
2453 3420 7.213678 TCTTTGGTTAGTTTAGGCAATTTTGG 58.786 34.615 0.00 0.00 0.00 3.28
2476 3443 2.993937 TGTTCAGTTTTGGTCGTTCCT 58.006 42.857 1.80 0.00 37.07 3.36
2699 3667 6.855763 TGTGGCTTTTGGAAAATAGATGAT 57.144 33.333 0.00 0.00 0.00 2.45
2702 3670 6.753744 GTGGCTTTTGGAAAATAGATGATGTC 59.246 38.462 0.00 0.00 0.00 3.06
3481 4456 7.433708 TTTAGAGATACCAAATGTGTGTGTG 57.566 36.000 0.00 0.00 0.00 3.82
3482 4457 4.973168 AGAGATACCAAATGTGTGTGTGT 58.027 39.130 0.00 0.00 0.00 3.72
3483 4458 4.756642 AGAGATACCAAATGTGTGTGTGTG 59.243 41.667 0.00 0.00 0.00 3.82
3484 4459 4.460263 AGATACCAAATGTGTGTGTGTGT 58.540 39.130 0.00 0.00 0.00 3.72
3486 4461 2.166829 ACCAAATGTGTGTGTGTGTGT 58.833 42.857 0.00 0.00 0.00 3.72
3487 4462 2.094803 ACCAAATGTGTGTGTGTGTGTG 60.095 45.455 0.00 0.00 0.00 3.82
3488 4463 2.094803 CCAAATGTGTGTGTGTGTGTGT 60.095 45.455 0.00 0.00 0.00 3.72
3489 4464 2.916089 CAAATGTGTGTGTGTGTGTGTG 59.084 45.455 0.00 0.00 0.00 3.82
3941 6898 6.149308 TGACTACTGACAAAGTGCAAATATGG 59.851 38.462 0.00 0.00 40.26 2.74
4863 7863 1.065126 AGGAGATTCTTTTGCGGGGAG 60.065 52.381 0.00 0.00 0.00 4.30
5228 8228 3.478857 TTGAGGCTTAGTTTTGTCGGA 57.521 42.857 0.00 0.00 0.00 4.55
5258 8258 1.936547 GGGAACGTCATCATCAGAAGC 59.063 52.381 0.00 0.00 0.00 3.86
5498 8510 1.527034 TGCATCAGCTCACTTTCACC 58.473 50.000 0.00 0.00 42.74 4.02
5559 8571 6.423905 GCTCTGCAAGGTACATCGATTAAATA 59.576 38.462 0.00 0.00 0.00 1.40
5616 8628 4.453751 AGCTAGAAGTAGAACTAGGACGG 58.546 47.826 0.00 0.00 37.25 4.79
5653 8667 2.018542 TTGGTGTATGCGCCTACTTC 57.981 50.000 21.08 14.38 45.25 3.01
5660 8674 0.977395 ATGCGCCTACTTCCCTATCC 59.023 55.000 4.18 0.00 0.00 2.59
5744 8758 3.057736 GCTTAATATGACCAGCATGCCTG 60.058 47.826 15.66 11.86 41.41 4.85
5755 8769 1.953231 GCATGCCTGCCCTTCCTTTC 61.953 60.000 6.36 0.00 42.88 2.62
5824 8838 8.398665 GGTTTACTCATAAATCTGGTCACAATC 58.601 37.037 0.00 0.00 32.91 2.67
5828 8842 6.825721 ACTCATAAATCTGGTCACAATCTTCC 59.174 38.462 0.00 0.00 0.00 3.46
5863 8877 0.908910 ACGTCCCATACCATTCAGCA 59.091 50.000 0.00 0.00 0.00 4.41
6019 9033 0.828022 ACTTCGACCAGTCCACACAA 59.172 50.000 0.00 0.00 0.00 3.33
6175 9189 4.115199 AGGGCGCCACCTCCATTC 62.115 66.667 30.85 7.16 35.43 2.67
6317 9331 4.857251 GGGACGCTTGGGATACTG 57.143 61.111 0.00 0.00 0.00 2.74
6715 9768 2.350738 CTGCTCTAGCTAGGCTCCC 58.649 63.158 25.11 10.95 40.44 4.30
6716 9769 0.468958 CTGCTCTAGCTAGGCTCCCA 60.469 60.000 25.11 13.87 40.44 4.37
6717 9770 0.757188 TGCTCTAGCTAGGCTCCCAC 60.757 60.000 25.11 9.41 40.44 4.61
6718 9771 1.468506 GCTCTAGCTAGGCTCCCACC 61.469 65.000 20.58 0.00 40.44 4.61
6779 9832 2.224606 TGTTCTGCTGCAAGGAAGAAG 58.775 47.619 3.02 0.00 29.53 2.85
6896 9950 2.661537 CGCCTGAGTGACGCAACA 60.662 61.111 0.00 0.00 0.00 3.33
6948 10006 3.046087 CACAGCCCGCTCACACAG 61.046 66.667 0.00 0.00 0.00 3.66
6986 10049 2.045634 GCCAGCCAGCAGACATCA 60.046 61.111 0.00 0.00 0.00 3.07
6994 10057 1.395954 CCAGCAGACATCATTCACACG 59.604 52.381 0.00 0.00 0.00 4.49
7016 10103 4.729918 CACTGCACAGGGCCTCCC 62.730 72.222 0.95 0.00 45.90 4.30
7026 10113 2.122769 GGCCTCCCCTCCTACTCC 60.123 72.222 0.00 0.00 0.00 3.85
7027 10114 2.717283 GGCCTCCCCTCCTACTCCT 61.717 68.421 0.00 0.00 0.00 3.69
7028 10115 1.369855 GGCCTCCCCTCCTACTCCTA 61.370 65.000 0.00 0.00 0.00 2.94
7029 10116 0.113580 GCCTCCCCTCCTACTCCTAG 59.886 65.000 0.00 0.00 0.00 3.02
7030 10117 1.536644 CCTCCCCTCCTACTCCTAGT 58.463 60.000 0.00 0.00 0.00 2.57
7031 10118 1.146152 CCTCCCCTCCTACTCCTAGTG 59.854 61.905 0.00 0.00 0.00 2.74
7112 10199 0.823356 CACCACCTTGTGAACAGGGG 60.823 60.000 15.24 9.16 46.27 4.79
7113 10200 0.991355 ACCACCTTGTGAACAGGGGA 60.991 55.000 15.24 0.00 46.27 4.81
7117 10204 1.380302 CTTGTGAACAGGGGAGGGG 59.620 63.158 0.00 0.00 0.00 4.79
7118 10205 2.771328 CTTGTGAACAGGGGAGGGGC 62.771 65.000 0.00 0.00 0.00 5.80
7119 10206 4.048470 GTGAACAGGGGAGGGGCC 62.048 72.222 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.801638 GCACGATGTCAATCTAGCCATCT 60.802 47.826 0.00 0.00 33.24 2.90
1 2 2.478134 GCACGATGTCAATCTAGCCATC 59.522 50.000 0.00 0.00 0.00 3.51
2 3 2.158914 TGCACGATGTCAATCTAGCCAT 60.159 45.455 0.00 0.00 32.39 4.40
3 4 1.206849 TGCACGATGTCAATCTAGCCA 59.793 47.619 0.00 0.00 32.39 4.75
4 5 1.863454 CTGCACGATGTCAATCTAGCC 59.137 52.381 0.00 0.00 32.39 3.93
5 6 1.260033 GCTGCACGATGTCAATCTAGC 59.740 52.381 0.00 0.00 33.38 3.42
6 7 2.538861 CAGCTGCACGATGTCAATCTAG 59.461 50.000 0.00 0.00 0.00 2.43
8 9 1.338484 ACAGCTGCACGATGTCAATCT 60.338 47.619 15.27 0.00 37.86 2.40
9 10 1.081892 ACAGCTGCACGATGTCAATC 58.918 50.000 15.27 0.00 37.86 2.67
10 11 3.238232 ACAGCTGCACGATGTCAAT 57.762 47.368 15.27 0.00 37.86 2.57
14 15 2.023771 CACGACAGCTGCACGATGT 61.024 57.895 30.57 13.14 46.62 3.06
15 16 2.774126 CACGACAGCTGCACGATG 59.226 61.111 30.57 22.23 34.52 3.84
16 17 3.114616 GCACGACAGCTGCACGAT 61.115 61.111 30.57 17.14 34.56 3.73
17 18 4.583866 TGCACGACAGCTGCACGA 62.584 61.111 30.57 13.14 39.76 4.35
21 22 1.016130 ACTACATGCACGACAGCTGC 61.016 55.000 15.27 5.81 34.99 5.25
22 23 0.717784 CACTACATGCACGACAGCTG 59.282 55.000 13.48 13.48 34.99 4.24
23 24 3.128259 CACTACATGCACGACAGCT 57.872 52.632 0.00 0.00 34.99 4.24
49 50 1.209261 TGGGATCGAAACTGCTATGCA 59.791 47.619 0.00 0.00 36.92 3.96
50 51 1.953559 TGGGATCGAAACTGCTATGC 58.046 50.000 0.00 0.00 0.00 3.14
51 52 5.050091 GTGTTATGGGATCGAAACTGCTATG 60.050 44.000 0.00 0.00 0.00 2.23
52 53 5.057149 GTGTTATGGGATCGAAACTGCTAT 58.943 41.667 0.00 0.00 0.00 2.97
53 54 4.439057 GTGTTATGGGATCGAAACTGCTA 58.561 43.478 0.00 0.00 0.00 3.49
54 55 3.270877 GTGTTATGGGATCGAAACTGCT 58.729 45.455 0.00 0.00 0.00 4.24
55 56 2.354821 GGTGTTATGGGATCGAAACTGC 59.645 50.000 0.00 0.00 0.00 4.40
56 57 2.943033 GGGTGTTATGGGATCGAAACTG 59.057 50.000 0.00 0.00 0.00 3.16
57 58 2.092592 GGGGTGTTATGGGATCGAAACT 60.093 50.000 0.00 0.00 0.00 2.66
58 59 2.294979 GGGGTGTTATGGGATCGAAAC 58.705 52.381 0.00 0.00 0.00 2.78
59 60 1.916874 TGGGGTGTTATGGGATCGAAA 59.083 47.619 0.00 0.00 0.00 3.46
60 61 1.210967 GTGGGGTGTTATGGGATCGAA 59.789 52.381 0.00 0.00 0.00 3.71
61 62 0.834612 GTGGGGTGTTATGGGATCGA 59.165 55.000 0.00 0.00 0.00 3.59
62 63 0.837272 AGTGGGGTGTTATGGGATCG 59.163 55.000 0.00 0.00 0.00 3.69
63 64 1.564348 ACAGTGGGGTGTTATGGGATC 59.436 52.381 0.00 0.00 0.00 3.36
96 97 1.750193 TATGCTGTTGCCTAGGTTGC 58.250 50.000 11.31 8.42 38.71 4.17
126 131 4.740268 TCAGAATGCATTGCAGAAATGTC 58.260 39.130 18.59 7.18 46.37 3.06
603 617 1.202687 CCGGTGATCACAGCCATGTAT 60.203 52.381 26.47 0.00 40.87 2.29
723 737 1.153005 GAGAGCCCAGCCCATGAAG 60.153 63.158 0.00 0.00 0.00 3.02
727 741 1.927527 AACAGAGAGCCCAGCCCAT 60.928 57.895 0.00 0.00 0.00 4.00
744 763 6.280855 TCAGTCTATCTTTCGGATCAACAA 57.719 37.500 0.00 0.00 35.98 2.83
751 770 4.220821 GCCCATATCAGTCTATCTTTCGGA 59.779 45.833 0.00 0.00 0.00 4.55
759 778 3.983410 ACTTTGGGCCCATATCAGTCTAT 59.017 43.478 29.23 0.62 0.00 1.98
760 779 3.136443 CACTTTGGGCCCATATCAGTCTA 59.864 47.826 29.23 3.48 0.00 2.59
761 780 2.092212 CACTTTGGGCCCATATCAGTCT 60.092 50.000 29.23 1.73 0.00 3.24
762 781 2.301346 CACTTTGGGCCCATATCAGTC 58.699 52.381 29.23 0.00 0.00 3.51
763 782 1.063717 CCACTTTGGGCCCATATCAGT 60.064 52.381 29.23 21.60 32.67 3.41
764 783 1.696063 CCACTTTGGGCCCATATCAG 58.304 55.000 29.23 20.92 32.67 2.90
765 784 3.922426 CCACTTTGGGCCCATATCA 57.078 52.632 29.23 7.80 32.67 2.15
775 804 1.237285 CGTTCAGGAGGCCACTTTGG 61.237 60.000 5.01 0.00 41.55 3.28
804 833 3.646534 CTTTTATCCCAATGGGCCTCTT 58.353 45.455 14.88 0.00 43.94 2.85
805 834 2.690936 GCTTTTATCCCAATGGGCCTCT 60.691 50.000 14.88 0.47 43.94 3.69
806 835 1.688735 GCTTTTATCCCAATGGGCCTC 59.311 52.381 14.88 0.00 43.94 4.70
807 836 1.291939 AGCTTTTATCCCAATGGGCCT 59.708 47.619 14.88 5.92 43.94 5.19
834 864 2.118404 CGCTCTCGGCTCTCCTTCT 61.118 63.158 0.00 0.00 39.13 2.85
964 994 4.951963 GAGAAGGATCGGCCGGCG 62.952 72.222 27.83 16.23 43.43 6.46
1054 1084 1.619827 TCGTTACCCTTGGTGGTACAG 59.380 52.381 0.00 0.00 41.80 2.74
1218 1248 3.063997 CGCATAGAAATGGTCACAGGAAC 59.936 47.826 0.00 0.00 33.38 3.62
1246 1276 8.365399 TGGTGCTATATGTATTCTCGAAAAAG 57.635 34.615 0.00 0.00 0.00 2.27
1306 1340 6.534298 AGATTACCAATCAGGGAACCAGGAA 61.534 44.000 0.00 0.00 45.14 3.36
1308 1342 3.203040 AGATTACCAATCAGGGAACCAGG 59.797 47.826 2.03 0.00 45.14 4.45
1346 1380 7.014422 ACAGGGTGTCGGAAAAATACAAAAATA 59.986 33.333 0.00 0.00 0.00 1.40
1347 1381 6.183360 ACAGGGTGTCGGAAAAATACAAAAAT 60.183 34.615 0.00 0.00 0.00 1.82
1360 1394 1.129917 TTACCAAACAGGGTGTCGGA 58.870 50.000 0.00 0.00 42.39 4.55
1425 1459 2.262211 GGCGGAAATTTGCAACTGATC 58.738 47.619 10.49 0.00 0.00 2.92
1429 1463 0.831711 AGGGGCGGAAATTTGCAACT 60.832 50.000 10.49 0.00 0.00 3.16
1431 1465 0.761802 AAAGGGGCGGAAATTTGCAA 59.238 45.000 10.49 0.00 0.00 4.08
1438 1472 1.534476 GGGGAAAAAGGGGCGGAAA 60.534 57.895 0.00 0.00 0.00 3.13
1680 1714 3.671716 AGACATTTACTTCCACGGTTCC 58.328 45.455 0.00 0.00 0.00 3.62
1681 1715 6.790285 TTTAGACATTTACTTCCACGGTTC 57.210 37.500 0.00 0.00 0.00 3.62
1682 1716 7.360607 CGAATTTAGACATTTACTTCCACGGTT 60.361 37.037 0.00 0.00 0.00 4.44
1683 1717 6.091713 CGAATTTAGACATTTACTTCCACGGT 59.908 38.462 0.00 0.00 0.00 4.83
1684 1718 6.091713 ACGAATTTAGACATTTACTTCCACGG 59.908 38.462 0.00 0.00 0.00 4.94
1685 1719 6.953743 CACGAATTTAGACATTTACTTCCACG 59.046 38.462 0.00 0.00 0.00 4.94
1686 1720 6.741358 GCACGAATTTAGACATTTACTTCCAC 59.259 38.462 0.00 0.00 0.00 4.02
1687 1721 6.653320 AGCACGAATTTAGACATTTACTTCCA 59.347 34.615 0.00 0.00 0.00 3.53
1741 1775 2.647802 ACAATGCCCCACCTAAGTAAGT 59.352 45.455 0.00 0.00 0.00 2.24
1742 1776 3.016736 CACAATGCCCCACCTAAGTAAG 58.983 50.000 0.00 0.00 0.00 2.34
1743 1777 2.645297 TCACAATGCCCCACCTAAGTAA 59.355 45.455 0.00 0.00 0.00 2.24
1744 1778 2.270858 TCACAATGCCCCACCTAAGTA 58.729 47.619 0.00 0.00 0.00 2.24
2238 2272 3.565307 ACAAGGCAGGATTGAAGAACAA 58.435 40.909 0.00 0.00 42.95 2.83
2239 2273 3.228188 ACAAGGCAGGATTGAAGAACA 57.772 42.857 0.00 0.00 0.00 3.18
2240 2274 5.393461 CCAATACAAGGCAGGATTGAAGAAC 60.393 44.000 14.33 0.00 32.16 3.01
2241 2275 4.706476 CCAATACAAGGCAGGATTGAAGAA 59.294 41.667 14.33 0.00 32.16 2.52
2242 2276 4.263905 ACCAATACAAGGCAGGATTGAAGA 60.264 41.667 14.33 0.00 32.16 2.87
2243 2277 4.019174 ACCAATACAAGGCAGGATTGAAG 58.981 43.478 14.33 3.92 32.16 3.02
2244 2278 4.046286 ACCAATACAAGGCAGGATTGAA 57.954 40.909 14.33 0.00 32.16 2.69
2245 2279 3.737559 ACCAATACAAGGCAGGATTGA 57.262 42.857 14.33 0.00 32.16 2.57
2246 2280 4.097892 GGTTACCAATACAAGGCAGGATTG 59.902 45.833 7.67 7.67 0.00 2.67
2247 2281 4.278310 GGTTACCAATACAAGGCAGGATT 58.722 43.478 0.00 0.00 0.00 3.01
2248 2282 3.684413 CGGTTACCAATACAAGGCAGGAT 60.684 47.826 1.13 0.00 0.00 3.24
2249 2283 2.355310 CGGTTACCAATACAAGGCAGGA 60.355 50.000 1.13 0.00 0.00 3.86
2250 2284 2.014128 CGGTTACCAATACAAGGCAGG 58.986 52.381 1.13 0.00 0.00 4.85
2284 2318 9.395707 GGTCTACGTGTTGATCATAATAAGTAG 57.604 37.037 0.00 3.81 36.15 2.57
2287 3254 7.921214 ACTGGTCTACGTGTTGATCATAATAAG 59.079 37.037 0.00 0.00 0.00 1.73
2453 3420 3.855379 GGAACGACCAAAACTGAACAAAC 59.145 43.478 0.00 0.00 38.79 2.93
2476 3443 0.460722 ATTGCAGCACAACAAGCACA 59.539 45.000 0.00 0.00 42.27 4.57
2699 3667 4.022676 TGTGTATAGAAGCTGTTGTCGACA 60.023 41.667 15.76 15.76 36.65 4.35
2702 3670 3.304559 GCTGTGTATAGAAGCTGTTGTCG 59.695 47.826 0.00 0.00 34.05 4.35
2866 3836 5.903010 TGGACCCTATAATAGACAAAGCTGA 59.097 40.000 0.00 0.00 0.00 4.26
2979 3954 3.126514 CGAGAGCATGCAAAACAAGATCT 59.873 43.478 21.98 10.29 44.81 2.75
4255 7244 8.415950 TTTAATTTATTTGTCCTGCAGGAGAA 57.584 30.769 34.90 34.90 46.49 2.87
4863 7863 1.728425 CGTTTTTACCACCGCTAGGAC 59.272 52.381 0.00 0.00 41.02 3.85
5189 8189 0.465824 ATTCTCTGCAGCCTCCATGC 60.466 55.000 9.47 0.00 44.11 4.06
5228 8228 0.762418 TGACGTTCCCAATGGAGTGT 59.238 50.000 0.00 0.00 43.07 3.55
5258 8258 4.876107 AGGTTGAAAATACCTGATAGTGCG 59.124 41.667 0.00 0.00 44.25 5.34
5498 8510 1.153289 CTGGGGGTCTTGCTCATCG 60.153 63.158 0.00 0.00 0.00 3.84
5559 8571 9.887629 CATCTAATTCTAGCATGAGGTTGATAT 57.112 33.333 0.00 0.00 0.00 1.63
5593 8605 5.130145 ACCGTCCTAGTTCTACTTCTAGCTA 59.870 44.000 0.00 0.00 34.18 3.32
5653 8667 4.637977 GTCTTGAGCTGAAAAAGGATAGGG 59.362 45.833 0.00 0.00 0.00 3.53
5660 8674 3.879295 TCCAGTGTCTTGAGCTGAAAAAG 59.121 43.478 0.00 0.00 32.39 2.27
5755 8769 3.016736 AGTAAAACCATCCTGGCATTCG 58.983 45.455 0.00 0.00 42.67 3.34
5828 8842 2.481449 GGACGTAACCATCCTAGCACAG 60.481 54.545 0.00 0.00 31.75 3.66
5863 8877 1.517832 CGGGCAGAGGTCGATTCTT 59.482 57.895 0.00 0.00 0.00 2.52
6019 9033 2.273912 GGAGTTGAGGTCCCGTCGT 61.274 63.158 0.00 0.00 0.00 4.34
6175 9189 3.853671 GCCATGTGAATTTTCGCTTACAG 59.146 43.478 5.55 0.00 38.47 2.74
6317 9331 4.772886 TGAAAAGGAGGGAGTATTAGCC 57.227 45.455 0.00 0.00 0.00 3.93
6575 9596 2.158325 AGACCAAGGGGCAAAATCAGAA 60.158 45.455 0.00 0.00 37.90 3.02
6604 9655 7.976414 ATGAATGGAATTTCCCTTTGACATA 57.024 32.000 12.90 0.00 36.07 2.29
6608 9659 6.931790 TCAATGAATGGAATTTCCCTTTGA 57.068 33.333 12.90 12.98 36.07 2.69
6613 9664 4.471025 AGGGTTCAATGAATGGAATTTCCC 59.529 41.667 12.90 2.46 36.07 3.97
6706 9759 2.670148 GGTGGTGGTGGGAGCCTAG 61.670 68.421 0.00 0.00 0.00 3.02
6707 9760 2.609610 GGTGGTGGTGGGAGCCTA 60.610 66.667 0.00 0.00 0.00 3.93
6708 9761 4.918360 TGGTGGTGGTGGGAGCCT 62.918 66.667 0.00 0.00 0.00 4.58
6709 9762 4.660938 GTGGTGGTGGTGGGAGCC 62.661 72.222 0.00 0.00 0.00 4.70
6710 9763 4.660938 GGTGGTGGTGGTGGGAGC 62.661 72.222 0.00 0.00 0.00 4.70
6711 9764 4.329545 CGGTGGTGGTGGTGGGAG 62.330 72.222 0.00 0.00 0.00 4.30
6712 9765 4.882396 TCGGTGGTGGTGGTGGGA 62.882 66.667 0.00 0.00 0.00 4.37
6713 9766 4.329545 CTCGGTGGTGGTGGTGGG 62.330 72.222 0.00 0.00 0.00 4.61
6718 9771 4.742201 CTCGGCTCGGTGGTGGTG 62.742 72.222 0.00 0.00 0.00 4.17
6763 9816 2.775890 TCTTCTTCTTCCTTGCAGCAG 58.224 47.619 0.00 0.00 0.00 4.24
6779 9832 3.552604 TGTGCGCTGGTATTTTTCTTC 57.447 42.857 9.73 0.00 0.00 2.87
6842 9896 4.152248 TGGGATCCACCTGTCAGG 57.848 61.111 17.88 17.88 42.49 3.86
6896 9950 1.745087 CGCATATTGCTGGGTTTCACT 59.255 47.619 0.00 0.00 42.25 3.41
6971 10034 1.400846 GTGAATGATGTCTGCTGGCTG 59.599 52.381 0.00 0.00 0.00 4.85
6980 10043 1.530720 TGTGTGCGTGTGAATGATGTC 59.469 47.619 0.00 0.00 0.00 3.06
6981 10044 1.264020 GTGTGTGCGTGTGAATGATGT 59.736 47.619 0.00 0.00 0.00 3.06
6986 10049 1.648720 GCAGTGTGTGCGTGTGAAT 59.351 52.632 0.00 0.00 43.99 2.57
7016 10103 3.868619 ACTAGCACTAGGAGTAGGAGG 57.131 52.381 9.41 0.00 37.49 4.30
7017 10104 5.556006 AGTACTAGCACTAGGAGTAGGAG 57.444 47.826 9.41 0.00 37.49 3.69
7018 10105 5.427806 TCAAGTACTAGCACTAGGAGTAGGA 59.572 44.000 9.41 3.06 37.49 2.94
7019 10106 5.528320 GTCAAGTACTAGCACTAGGAGTAGG 59.472 48.000 9.41 0.93 37.49 3.18
7021 10108 5.435291 GGTCAAGTACTAGCACTAGGAGTA 58.565 45.833 9.41 0.00 37.49 2.59
7022 10109 4.271661 GGTCAAGTACTAGCACTAGGAGT 58.728 47.826 9.41 0.55 37.49 3.85
7023 10110 3.312973 CGGTCAAGTACTAGCACTAGGAG 59.687 52.174 9.41 0.00 37.49 3.69
7024 10111 3.054875 TCGGTCAAGTACTAGCACTAGGA 60.055 47.826 9.41 0.00 37.49 2.94
7025 10112 3.276857 TCGGTCAAGTACTAGCACTAGG 58.723 50.000 9.41 0.00 37.49 3.02
7026 10113 4.575236 TCATCGGTCAAGTACTAGCACTAG 59.425 45.833 0.00 3.10 39.04 2.57
7027 10114 4.520179 TCATCGGTCAAGTACTAGCACTA 58.480 43.478 0.00 0.00 0.00 2.74
7028 10115 3.353557 TCATCGGTCAAGTACTAGCACT 58.646 45.455 0.00 0.00 0.00 4.40
7029 10116 3.777465 TCATCGGTCAAGTACTAGCAC 57.223 47.619 0.00 0.00 0.00 4.40
7030 10117 3.951680 TCATCATCGGTCAAGTACTAGCA 59.048 43.478 0.00 0.00 0.00 3.49
7031 10118 4.569761 TCATCATCGGTCAAGTACTAGC 57.430 45.455 0.00 0.00 0.00 3.42


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.